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E39 (1997 - 2003) The BMW 5-Series (E39 chassis) was introduced in the United States as a 1997 model year car and lasted until the 2004 when the E60 chassis was released. The United States saw several variations including the 525i, 528i, 530i and 540i. -- View the E39 Wiki

Yes checking the ATF level is on the list. It's just more involved and requires more planning. Alternator and battery checks are relatively easy. (Easy to sneak in without the wife tapping her foot...)

I do agree that if the tranny is dry and there are no other shifting issues, I find it hard to believe its related to fluid. (Which is the case here)

Relative to the water intrusion theory, I checked for wetness in the passenger footwells. I pulled up some carpet in the rear but did not find any damp areas. (Did a vapor barrier fix to this door back in May). The front passenger door did not feel wet so I did not pull that carpet up.

I did pull apart the tub that houses the trans ecu. I did not find any standing water but I did see signs of water intrusion. (The outermost screw closest to the windshield). I did some temporary fix until I can get some permatex. Non of those wires showed any signs of water damage. All seemed tight.

I did find a lot of junk in the air filter drain tubes.

I will plan for a deeper dive into the footwells after I wash the car again.